Properly meshing a metaball
I think I'm starting to understand what is going on. Correct me if I'm wrong, but I think you parented the meta-ball to the cube to change it to the desired shape.
A mesh with this shape is inside the weird thing with the seams.
I converted your meta-ball in the file to a mesh. Then selected it and removed it as a child from the cube. 3D viewport &gt; Object &gt; Parent &gt; Clear Parent (or press Alt+P). The thing with the seams disappears, and then i'm left with the mesh I believe you want.
Since this was, as you described it, a simple test, I hope (but am unable to tell if) it also works in a more complicated scenario.